Blog #1: Optimizing Organic Synthesis

When I arrived at school this summer to begin conducting research in the lab, I originally intended to explore chemical synthesis with the microwave, a tool that is widely used in the biosciences to decrease chemical reaction times and increase product yields. I proposed optimizing click reactions, which are reactions that effectively connect two large molecules through a quick and stable mechanism. After talking more with my advisor, my focus shifted.

My summer project focused on synthesizing molecules known as “profluorophores.” Profluorophores are molecules that, on their own, do not emit fluorescence. However, when a profluorophore is linked with another molecule (normally through a click mechanism), the molecule becomes fluorescent. Thus, by ligating a profluorophore with another molecule of interest, scientists can track the location and movement of the molecule of interest without saturating the entire environment with fluorescence.

This summer, my goal was to synthesize and isolate a few of these profluorophores to further use for fluorescent click reactions. As I progressed toward this goal, I worked on small side projects with other lab members as well. Such projects included working with unnatural amino acids and cloning DNA sequences using transformed bacterial cells, both of which are major research areas in my professor’s lab. In performing these side experiments, I became familiar with nearly all of the instruments and techniques we use in our lab, including bacterial transformations via electroporation, gel electrophoresis, UV gel imaging, and so many more.

In the first week of my research, I must admit that I had some difficulties. Because I had entered the summer with limited lab experience, I was very dependent on my lab mates and my lab’s graduate student. As I attempted to make my first profluorophore, I needed help at every step. Early on, I also had trouble obtaining good data from the NMR Spectrometer, as the computer program sometimes had glitches that I did not know how to troubleshoot. The NMR Spectrometer is basically a big instrument that uses magnetic fields to generate a spectrum of peaks, which I can then use to verify the structure of my compound. My first profluorophore needed to be checked by the NMR at every step before I could move on to the next step; so, when I can’t get the NMR to work, I’m left with nothing to do until I can obtain a decent NMR spectrum.┬áNevertheless, by the end of the second week, I had synthesized, isolated, and obtained a good NMR spectrum for my first profluorophore.

As I did my research the first few weeks, I became increasingly aware of the fact that scientific research takes a very very long time to come to fruition.When I accounted for my own mistakes, technological complications, and reactions that just didn’t go as planned, I learned that research is a long process. And whenever things don’t go as planned, you have to take a step back and start again, which I had to do many times during the summer.